Multiple sequence alignment - TraesCS3A01G373700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G373700 chr3A 100.000 2401 0 0 1 2401 623611127 623608727 0.000000e+00 4434
1 TraesCS3A01G373700 chr3A 88.901 946 94 8 148 1087 625209673 625210613 0.000000e+00 1155
2 TraesCS3A01G373700 chr3A 74.268 820 165 35 209 1008 598554286 598553493 1.080000e-78 303
3 TraesCS3A01G373700 chr3A 75.156 640 123 27 379 1012 448702591 448701982 3.930000e-68 268
4 TraesCS3A01G373700 chr3A 71.867 814 160 53 223 1003 484636195 484636972 1.140000e-38 171
5 TraesCS3A01G373700 chr3B 91.157 2273 102 39 55 2265 641661676 641659441 0.000000e+00 2992
6 TraesCS3A01G373700 chr3B 87.553 940 110 6 162 1100 644171754 644172687 0.000000e+00 1081
7 TraesCS3A01G373700 chr3B 74.450 818 161 38 209 1008 602332037 602331250 2.320000e-80 309
8 TraesCS3A01G373700 chr3B 74.450 818 161 38 209 1008 602353119 602352332 2.320000e-80 309
9 TraesCS3A01G373700 chr3B 75.039 633 118 29 379 1003 431040820 431040220 8.520000e-65 257
10 TraesCS3A01G373700 chr3B 92.414 145 9 2 2258 2401 641658001 641657858 3.130000e-49 206
11 TraesCS3A01G373700 chr3B 92.029 138 8 1 2262 2396 641658679 641658542 8.760000e-45 191
12 TraesCS3A01G373700 chr3D 94.780 1590 44 20 97 1674 480843358 480841796 0.000000e+00 2440
13 TraesCS3A01G373700 chr3D 88.387 930 100 5 162 1087 482190151 482191076 0.000000e+00 1112
14 TraesCS3A01G373700 chr3D 91.472 727 38 8 1679 2398 480841764 480841055 0.000000e+00 977
15 TraesCS3A01G373700 chr3D 74.421 821 162 37 209 1008 455870522 455869729 2.320000e-80 309
16 TraesCS3A01G373700 chr3D 73.848 803 148 48 223 1003 331657954 331657192 1.830000e-66 263
17 TraesCS3A01G373700 chr3D 91.034 145 11 2 2258 2401 480840428 480840285 6.770000e-46 195


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G373700 chr3A 623608727 623611127 2400 True 4434.000000 4434 100.000000 1 2401 1 chr3A.!!$R3 2400
1 TraesCS3A01G373700 chr3A 625209673 625210613 940 False 1155.000000 1155 88.901000 148 1087 1 chr3A.!!$F2 939
2 TraesCS3A01G373700 chr3A 598553493 598554286 793 True 303.000000 303 74.268000 209 1008 1 chr3A.!!$R2 799
3 TraesCS3A01G373700 chr3A 448701982 448702591 609 True 268.000000 268 75.156000 379 1012 1 chr3A.!!$R1 633
4 TraesCS3A01G373700 chr3B 641657858 641661676 3818 True 1129.666667 2992 91.866667 55 2401 3 chr3B.!!$R4 2346
5 TraesCS3A01G373700 chr3B 644171754 644172687 933 False 1081.000000 1081 87.553000 162 1100 1 chr3B.!!$F1 938
6 TraesCS3A01G373700 chr3B 602331250 602332037 787 True 309.000000 309 74.450000 209 1008 1 chr3B.!!$R2 799
7 TraesCS3A01G373700 chr3B 602352332 602353119 787 True 309.000000 309 74.450000 209 1008 1 chr3B.!!$R3 799
8 TraesCS3A01G373700 chr3B 431040220 431040820 600 True 257.000000 257 75.039000 379 1003 1 chr3B.!!$R1 624
9 TraesCS3A01G373700 chr3D 480840285 480843358 3073 True 1204.000000 2440 92.428667 97 2401 3 chr3D.!!$R3 2304
10 TraesCS3A01G373700 chr3D 482190151 482191076 925 False 1112.000000 1112 88.387000 162 1087 1 chr3D.!!$F1 925
11 TraesCS3A01G373700 chr3D 455869729 455870522 793 True 309.000000 309 74.421000 209 1008 1 chr3D.!!$R2 799
12 TraesCS3A01G373700 chr3D 331657192 331657954 762 True 263.000000 263 73.848000 223 1003 1 chr3D.!!$R1 780

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
42 43 1.134936 ACAATCGGCATACTACACGCA 60.135 47.619 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1743 0.033503 TGCCCGTGATACAGGAGAGA 60.034 55.0 0.0 0.0 0.0 3.1 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.906660 AATTTCAAAACATGTCATACGTACAAT 57.093 25.926 0.00 0.00 0.00 2.71
27 28 8.942669 TTTCAAAACATGTCATACGTACAATC 57.057 30.769 0.00 0.00 0.00 2.67
28 29 6.757162 TCAAAACATGTCATACGTACAATCG 58.243 36.000 0.00 0.00 0.00 3.34
29 30 5.712217 AAACATGTCATACGTACAATCGG 57.288 39.130 0.00 0.00 34.94 4.18
30 31 3.120792 ACATGTCATACGTACAATCGGC 58.879 45.455 0.00 0.00 34.94 5.54
31 32 2.943449 TGTCATACGTACAATCGGCA 57.057 45.000 0.00 0.00 34.94 5.69
32 33 3.446310 TGTCATACGTACAATCGGCAT 57.554 42.857 0.00 0.00 34.94 4.40
33 34 4.571372 TGTCATACGTACAATCGGCATA 57.429 40.909 0.00 0.00 34.94 3.14
34 35 4.292599 TGTCATACGTACAATCGGCATAC 58.707 43.478 0.00 0.00 34.94 2.39
35 36 4.037089 TGTCATACGTACAATCGGCATACT 59.963 41.667 0.00 0.00 34.94 2.12
36 37 5.239087 TGTCATACGTACAATCGGCATACTA 59.761 40.000 0.00 0.00 34.94 1.82
37 38 5.566774 GTCATACGTACAATCGGCATACTAC 59.433 44.000 0.00 0.00 34.94 2.73
38 39 5.239087 TCATACGTACAATCGGCATACTACA 59.761 40.000 0.00 0.00 34.94 2.74
39 40 3.699067 ACGTACAATCGGCATACTACAC 58.301 45.455 0.00 0.00 34.94 2.90
40 41 2.717519 CGTACAATCGGCATACTACACG 59.282 50.000 0.00 0.00 0.00 4.49
41 42 1.567504 ACAATCGGCATACTACACGC 58.432 50.000 0.00 0.00 0.00 5.34
42 43 1.134936 ACAATCGGCATACTACACGCA 60.135 47.619 0.00 0.00 0.00 5.24
43 44 1.522676 CAATCGGCATACTACACGCAG 59.477 52.381 0.00 0.00 0.00 5.18
45 46 1.381522 TCGGCATACTACACGCAGTA 58.618 50.000 0.00 0.00 41.61 2.74
46 47 1.951602 TCGGCATACTACACGCAGTAT 59.048 47.619 0.42 0.42 41.61 2.12
47 48 3.140623 TCGGCATACTACACGCAGTATA 58.859 45.455 5.03 0.00 41.61 1.47
48 49 3.058708 TCGGCATACTACACGCAGTATAC 60.059 47.826 0.00 0.00 41.61 1.47
49 50 3.231965 GGCATACTACACGCAGTATACG 58.768 50.000 0.00 0.00 41.61 3.06
50 51 3.304257 GGCATACTACACGCAGTATACGT 60.304 47.826 0.00 0.00 41.61 3.57
51 52 4.083855 GGCATACTACACGCAGTATACGTA 60.084 45.833 0.00 0.00 41.61 3.57
52 53 4.842911 GCATACTACACGCAGTATACGTAC 59.157 45.833 0.00 0.00 41.61 3.67
53 54 5.558844 GCATACTACACGCAGTATACGTACA 60.559 44.000 0.00 0.00 41.61 2.90
65 66 6.953743 GCAGTATACGTACAATTGTGTTTCTG 59.046 38.462 21.42 17.62 39.30 3.02
89 90 6.018588 TGGATAAGATACAATTTAACACGGCG 60.019 38.462 4.80 4.80 0.00 6.46
143 145 1.583967 GATCGACGTGCTCCTGACG 60.584 63.158 0.00 0.00 42.62 4.35
783 820 3.531207 CCGCCGATGGAGAGCAGA 61.531 66.667 0.00 0.00 0.00 4.26
1048 1091 3.361158 CGGCCATTGTCACCGCAA 61.361 61.111 2.24 0.00 40.55 4.85
1073 1116 0.031994 AACAGCATTGCCGGAAACAC 59.968 50.000 5.05 0.00 0.00 3.32
1148 1192 2.334977 TGCTGGAGAAGGTTCTTGGTA 58.665 47.619 0.00 0.00 37.73 3.25
1403 1453 1.902765 ATGACGGTGCAGGCTGATCA 61.903 55.000 20.86 12.80 0.00 2.92
1542 1592 6.340962 TGTTCTCCTATGAAGTTTCTTCGA 57.659 37.500 5.28 0.00 0.00 3.71
1543 1593 6.157211 TGTTCTCCTATGAAGTTTCTTCGAC 58.843 40.000 5.28 0.00 0.00 4.20
1547 1597 3.548268 CCTATGAAGTTTCTTCGACTCGC 59.452 47.826 0.00 0.00 0.00 5.03
1593 1644 0.310854 GTAATACTGCCGCAATGCCC 59.689 55.000 0.00 0.00 0.00 5.36
1594 1645 0.182537 TAATACTGCCGCAATGCCCT 59.817 50.000 0.00 0.00 0.00 5.19
1636 1695 4.782195 GCGAGTATGACCAAATTTGCTACG 60.782 45.833 12.92 9.57 0.00 3.51
1637 1696 4.328983 CGAGTATGACCAAATTTGCTACGT 59.671 41.667 12.92 5.13 0.00 3.57
1638 1697 5.517411 CGAGTATGACCAAATTTGCTACGTA 59.483 40.000 12.92 8.50 0.00 3.57
1639 1698 6.507456 CGAGTATGACCAAATTTGCTACGTAC 60.507 42.308 12.92 17.53 0.00 3.67
1640 1699 6.403878 AGTATGACCAAATTTGCTACGTACT 58.596 36.000 22.07 22.07 0.00 2.73
1641 1700 7.549839 AGTATGACCAAATTTGCTACGTACTA 58.450 34.615 24.09 9.42 31.32 1.82
1653 1719 8.498054 TTTGCTACGTACTAGTACTTATCTGT 57.502 34.615 26.36 18.65 34.04 3.41
1669 1735 7.931275 ACTTATCTGTTTGGAAGTTTGAAGTC 58.069 34.615 0.00 0.00 0.00 3.01
1674 1740 3.662759 TTGGAAGTTTGAAGTCCCAGT 57.337 42.857 0.00 0.00 0.00 4.00
1675 1741 3.662759 TGGAAGTTTGAAGTCCCAGTT 57.337 42.857 0.00 0.00 0.00 3.16
1677 1743 3.288092 GGAAGTTTGAAGTCCCAGTTGT 58.712 45.455 0.00 0.00 0.00 3.32
1695 1788 0.386113 GTCTCTCCTGTATCACGGGC 59.614 60.000 0.00 0.00 44.40 6.13
1697 1790 0.103208 CTCTCCTGTATCACGGGCAC 59.897 60.000 0.00 0.00 44.40 5.01
1700 1794 0.908910 TCCTGTATCACGGGCACATT 59.091 50.000 0.00 0.00 44.40 2.71
1721 1815 2.188817 GTGGAACTGAGTGGATACCCT 58.811 52.381 0.00 0.00 0.00 4.34
1751 1845 2.367772 GTCTGAATCGTGTCGATCTCG 58.632 52.381 5.15 0.00 46.30 4.04
1753 1847 2.104901 CTGAATCGTGTCGATCTCGTG 58.895 52.381 5.15 0.00 46.30 4.35
1768 1862 0.249447 TCGTGCAGTCCTTGTCAGTG 60.249 55.000 0.00 0.00 0.00 3.66
1769 1863 1.835483 CGTGCAGTCCTTGTCAGTGC 61.835 60.000 0.00 0.00 40.16 4.40
1772 1866 0.250038 GCAGTCCTTGTCAGTGCTGA 60.250 55.000 0.00 0.00 37.25 4.26
1786 1880 2.674852 AGTGCTGAATTGTGACGCATAG 59.325 45.455 0.00 0.00 32.75 2.23
1816 1910 9.949174 TCCATATTTATCAATTCAATGTGTTCG 57.051 29.630 0.00 0.00 0.00 3.95
1817 1911 9.734620 CCATATTTATCAATTCAATGTGTTCGT 57.265 29.630 0.00 0.00 0.00 3.85
1843 1938 6.447162 GTGGAACCCAATGAACTTAAAGAAG 58.553 40.000 0.00 0.00 34.18 2.85
1886 1981 7.809331 TCAAAGTGTCTGCATTATCAATTCAAC 59.191 33.333 0.00 0.00 0.00 3.18
1888 1983 5.643348 AGTGTCTGCATTATCAATTCAACGA 59.357 36.000 0.00 0.00 0.00 3.85
1889 1984 6.317140 AGTGTCTGCATTATCAATTCAACGAT 59.683 34.615 0.00 0.00 0.00 3.73
1891 1986 7.164826 GTGTCTGCATTATCAATTCAACGATTC 59.835 37.037 0.00 0.00 0.00 2.52
1892 1987 7.148272 TGTCTGCATTATCAATTCAACGATTCA 60.148 33.333 0.00 0.00 0.00 2.57
1893 1988 7.375280 GTCTGCATTATCAATTCAACGATTCAG 59.625 37.037 0.00 0.00 0.00 3.02
1894 1989 5.972973 TGCATTATCAATTCAACGATTCAGC 59.027 36.000 0.00 0.00 0.00 4.26
1895 1990 5.400485 GCATTATCAATTCAACGATTCAGCC 59.600 40.000 0.00 0.00 0.00 4.85
1896 1991 6.497437 CATTATCAATTCAACGATTCAGCCA 58.503 36.000 0.00 0.00 0.00 4.75
1897 1992 6.698008 TTATCAATTCAACGATTCAGCCAT 57.302 33.333 0.00 0.00 0.00 4.40
1898 1993 5.587388 ATCAATTCAACGATTCAGCCATT 57.413 34.783 0.00 0.00 0.00 3.16
1899 1994 4.735985 TCAATTCAACGATTCAGCCATTG 58.264 39.130 0.00 0.00 0.00 2.82
1900 1995 4.458642 TCAATTCAACGATTCAGCCATTGA 59.541 37.500 0.00 0.00 0.00 2.57
1901 1996 4.627611 ATTCAACGATTCAGCCATTGAG 57.372 40.909 0.00 0.00 37.07 3.02
1912 2007 1.089920 GCCATTGAGCCTGTAGTGTG 58.910 55.000 0.00 0.00 0.00 3.82
1924 2019 3.318017 CTGTAGTGTGTAGTGGACAAGC 58.682 50.000 0.00 0.00 40.66 4.01
2036 2131 2.092211 GGCTAAACACGACGATGAACAG 59.908 50.000 0.00 0.00 0.00 3.16
2063 2158 1.650528 GGATGGCCCTAGCTAGATGT 58.349 55.000 22.70 3.26 39.73 3.06
2064 2159 1.981495 GGATGGCCCTAGCTAGATGTT 59.019 52.381 22.70 2.77 39.73 2.71
2069 2164 3.181451 TGGCCCTAGCTAGATGTTTGATG 60.181 47.826 22.70 1.70 39.73 3.07
2111 2206 6.405065 CCAATGGACTGTGAAATGGACAATAG 60.405 42.308 0.00 0.00 0.00 1.73
2116 2211 1.676006 GTGAAATGGACAATAGGCCGG 59.324 52.381 0.00 0.00 0.00 6.13
2174 2269 6.099269 TCCCCAACCTGACAATAACTCTATAC 59.901 42.308 0.00 0.00 0.00 1.47
2253 2348 9.527157 TCATAAAGGACATGATTGGAAGTTTTA 57.473 29.630 0.00 0.00 0.00 1.52
2295 3155 1.702491 GGAACGGCCGCACTGATAAC 61.702 60.000 28.58 5.82 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.906660 ATTGTACGTATGACATGTTTTGAAATT 57.093 25.926 0.00 0.00 0.00 1.82
1 2 9.554724 GATTGTACGTATGACATGTTTTGAAAT 57.445 29.630 0.00 0.00 0.00 2.17
2 3 7.742525 CGATTGTACGTATGACATGTTTTGAAA 59.257 33.333 0.00 0.00 0.00 2.69
3 4 7.230914 CGATTGTACGTATGACATGTTTTGAA 58.769 34.615 0.00 0.00 0.00 2.69
4 5 6.183360 CCGATTGTACGTATGACATGTTTTGA 60.183 38.462 0.00 0.00 0.00 2.69
5 6 5.957220 CCGATTGTACGTATGACATGTTTTG 59.043 40.000 0.00 0.00 0.00 2.44
6 7 5.446741 GCCGATTGTACGTATGACATGTTTT 60.447 40.000 0.00 0.00 0.00 2.43
7 8 4.033587 GCCGATTGTACGTATGACATGTTT 59.966 41.667 0.00 0.00 0.00 2.83
8 9 3.554324 GCCGATTGTACGTATGACATGTT 59.446 43.478 0.00 0.00 0.00 2.71
9 10 3.120792 GCCGATTGTACGTATGACATGT 58.879 45.455 0.00 0.00 0.00 3.21
10 11 3.120041 TGCCGATTGTACGTATGACATG 58.880 45.455 0.00 0.00 0.00 3.21
11 12 3.446310 TGCCGATTGTACGTATGACAT 57.554 42.857 0.00 0.00 0.00 3.06
12 13 2.943449 TGCCGATTGTACGTATGACA 57.057 45.000 0.00 0.00 0.00 3.58
13 14 4.543692 AGTATGCCGATTGTACGTATGAC 58.456 43.478 0.00 0.00 0.00 3.06
14 15 4.841443 AGTATGCCGATTGTACGTATGA 57.159 40.909 0.00 0.00 0.00 2.15
15 16 5.341462 GTGTAGTATGCCGATTGTACGTATG 59.659 44.000 0.00 0.00 0.00 2.39
16 17 5.455392 GTGTAGTATGCCGATTGTACGTAT 58.545 41.667 0.00 0.00 0.00 3.06
17 18 4.552572 CGTGTAGTATGCCGATTGTACGTA 60.553 45.833 0.00 0.00 0.00 3.57
18 19 3.699067 GTGTAGTATGCCGATTGTACGT 58.301 45.455 0.00 0.00 0.00 3.57
19 20 2.717519 CGTGTAGTATGCCGATTGTACG 59.282 50.000 0.00 0.00 0.00 3.67
20 21 2.470257 GCGTGTAGTATGCCGATTGTAC 59.530 50.000 0.00 0.00 35.18 2.90
21 22 2.099427 TGCGTGTAGTATGCCGATTGTA 59.901 45.455 0.00 0.00 40.72 2.41
22 23 1.134936 TGCGTGTAGTATGCCGATTGT 60.135 47.619 0.00 0.00 40.72 2.71
23 24 1.522676 CTGCGTGTAGTATGCCGATTG 59.477 52.381 0.00 0.00 40.72 2.67
24 25 1.136305 ACTGCGTGTAGTATGCCGATT 59.864 47.619 0.00 0.00 40.72 3.34
25 26 0.744874 ACTGCGTGTAGTATGCCGAT 59.255 50.000 0.00 0.00 40.72 4.18
26 27 1.381522 TACTGCGTGTAGTATGCCGA 58.618 50.000 0.00 0.00 40.72 5.54
27 28 2.417339 ATACTGCGTGTAGTATGCCG 57.583 50.000 9.41 0.00 41.17 5.69
28 29 3.231965 CGTATACTGCGTGTAGTATGCC 58.768 50.000 17.46 9.14 42.31 4.40
29 30 3.881795 ACGTATACTGCGTGTAGTATGC 58.118 45.455 17.46 15.37 42.31 3.14
30 31 5.977731 TGTACGTATACTGCGTGTAGTATG 58.022 41.667 17.46 7.19 42.31 2.39
31 32 6.603237 TTGTACGTATACTGCGTGTAGTAT 57.397 37.500 13.80 13.80 44.04 2.12
32 33 6.603237 ATTGTACGTATACTGCGTGTAGTA 57.397 37.500 0.00 0.29 42.87 1.82
33 34 4.944962 TTGTACGTATACTGCGTGTAGT 57.055 40.909 0.00 0.00 42.87 2.73
34 35 5.740569 ACAATTGTACGTATACTGCGTGTAG 59.259 40.000 9.97 0.00 42.87 2.74
35 36 5.512434 CACAATTGTACGTATACTGCGTGTA 59.488 40.000 11.53 0.00 42.87 2.90
36 37 4.325204 CACAATTGTACGTATACTGCGTGT 59.675 41.667 11.53 0.00 42.87 4.49
37 38 4.325204 ACACAATTGTACGTATACTGCGTG 59.675 41.667 11.53 5.60 42.87 5.34
38 39 4.487948 ACACAATTGTACGTATACTGCGT 58.512 39.130 11.53 0.00 45.11 5.24
39 40 5.444586 AACACAATTGTACGTATACTGCG 57.555 39.130 11.53 0.00 33.55 5.18
40 41 6.953743 CAGAAACACAATTGTACGTATACTGC 59.046 38.462 11.53 0.00 33.55 4.40
41 42 7.329962 TCCAGAAACACAATTGTACGTATACTG 59.670 37.037 11.53 14.04 33.55 2.74
42 43 7.380536 TCCAGAAACACAATTGTACGTATACT 58.619 34.615 11.53 4.25 33.55 2.12
43 44 7.585286 TCCAGAAACACAATTGTACGTATAC 57.415 36.000 11.53 0.00 33.55 1.47
44 45 9.872721 TTATCCAGAAACACAATTGTACGTATA 57.127 29.630 11.53 0.00 33.55 1.47
45 46 8.780846 TTATCCAGAAACACAATTGTACGTAT 57.219 30.769 11.53 0.00 33.55 3.06
46 47 8.089597 TCTTATCCAGAAACACAATTGTACGTA 58.910 33.333 11.53 0.00 33.55 3.57
47 48 6.932400 TCTTATCCAGAAACACAATTGTACGT 59.068 34.615 11.53 3.01 33.55 3.57
48 49 7.359262 TCTTATCCAGAAACACAATTGTACG 57.641 36.000 11.53 2.29 33.55 3.67
50 51 9.952030 TGTATCTTATCCAGAAACACAATTGTA 57.048 29.630 11.53 0.00 34.16 2.41
51 52 8.862325 TGTATCTTATCCAGAAACACAATTGT 57.138 30.769 4.92 4.92 34.16 2.71
65 66 6.201425 TCGCCGTGTTAAATTGTATCTTATCC 59.799 38.462 0.00 0.00 0.00 2.59
81 82 1.730121 CGTGTAGTATGTCGCCGTGTT 60.730 52.381 0.00 0.00 0.00 3.32
85 86 1.200474 CTGCGTGTAGTATGTCGCCG 61.200 60.000 5.98 0.00 46.57 6.46
89 90 3.421231 GCGAATACTGCGTGTAGTATGTC 59.579 47.826 10.71 9.47 41.70 3.06
143 145 2.412847 GCTGATGTTGTTAACTGCGTCC 60.413 50.000 7.22 0.00 0.00 4.79
765 802 3.842923 CTGCTCTCCATCGGCGGT 61.843 66.667 7.21 0.00 0.00 5.68
1047 1090 0.108992 CGGCAATGCTGTTGCTCATT 60.109 50.000 21.10 0.00 44.36 2.57
1048 1091 1.509463 CGGCAATGCTGTTGCTCAT 59.491 52.632 21.10 0.00 44.36 2.90
1073 1116 2.712057 AACAAAGATGGCGAGCAAAG 57.288 45.000 0.00 0.00 0.00 2.77
1148 1192 6.376581 GGGTTCTACTGGCTATATATACACGT 59.623 42.308 0.00 0.00 0.00 4.49
1542 1592 0.732880 CACCGAACGATTCAGCGAGT 60.733 55.000 0.00 0.00 34.83 4.18
1543 1593 1.991430 CACCGAACGATTCAGCGAG 59.009 57.895 0.00 0.00 34.83 5.03
1547 1597 1.006825 TCACGCACCGAACGATTCAG 61.007 55.000 0.00 0.00 0.00 3.02
1593 1644 3.601586 CGCGCGTATTGTGGAAAGATAAG 60.602 47.826 24.19 0.00 0.00 1.73
1594 1645 2.283086 CGCGCGTATTGTGGAAAGATAA 59.717 45.455 24.19 0.00 0.00 1.75
1638 1697 9.490379 CAAACTTCCAAACAGATAAGTACTAGT 57.510 33.333 0.00 0.00 32.09 2.57
1639 1698 9.706691 TCAAACTTCCAAACAGATAAGTACTAG 57.293 33.333 0.00 0.00 32.09 2.57
1641 1700 8.974060 TTCAAACTTCCAAACAGATAAGTACT 57.026 30.769 0.00 0.00 32.09 2.73
1653 1719 3.976015 ACTGGGACTTCAAACTTCCAAA 58.024 40.909 0.00 0.00 0.00 3.28
1669 1735 3.099905 TGATACAGGAGAGACAACTGGG 58.900 50.000 0.00 0.00 36.57 4.45
1674 1740 2.100197 CCCGTGATACAGGAGAGACAA 58.900 52.381 0.00 0.00 0.00 3.18
1675 1741 1.763968 CCCGTGATACAGGAGAGACA 58.236 55.000 0.00 0.00 0.00 3.41
1677 1743 0.033503 TGCCCGTGATACAGGAGAGA 60.034 55.000 0.00 0.00 0.00 3.10
1695 1788 2.849942 TCCACTCAGTTCCACAATGTG 58.150 47.619 6.37 6.37 0.00 3.21
1697 1790 3.941483 GGTATCCACTCAGTTCCACAATG 59.059 47.826 0.00 0.00 0.00 2.82
1700 1794 1.906574 GGGTATCCACTCAGTTCCACA 59.093 52.381 0.00 0.00 0.00 4.17
1721 1815 5.229260 CGACACGATTCAGACGAAATGATAA 59.771 40.000 0.00 0.00 34.01 1.75
1751 1845 0.533755 AGCACTGACAAGGACTGCAC 60.534 55.000 0.00 0.00 0.00 4.57
1753 1847 0.250038 TCAGCACTGACAAGGACTGC 60.250 55.000 0.00 0.00 34.14 4.40
1768 1862 2.009774 ACCTATGCGTCACAATTCAGC 58.990 47.619 0.00 0.00 0.00 4.26
1769 1863 3.002791 ACACCTATGCGTCACAATTCAG 58.997 45.455 0.00 0.00 0.00 3.02
1772 1866 2.290008 TGGACACCTATGCGTCACAATT 60.290 45.455 0.00 0.00 33.66 2.32
1786 1880 9.467258 CACATTGAATTGATAAATATGGACACC 57.533 33.333 0.00 0.00 0.00 4.16
1813 1907 0.474614 TCATTGGGTTCCACCACGAA 59.525 50.000 0.00 0.00 41.02 3.85
1814 1908 0.474614 TTCATTGGGTTCCACCACGA 59.525 50.000 0.00 0.00 41.02 4.35
1815 1909 0.596082 GTTCATTGGGTTCCACCACG 59.404 55.000 0.00 0.00 41.02 4.94
1816 1910 1.995376 AGTTCATTGGGTTCCACCAC 58.005 50.000 0.00 0.00 41.02 4.16
1817 1911 2.765689 AAGTTCATTGGGTTCCACCA 57.234 45.000 0.00 0.00 41.02 4.17
1818 1912 4.830600 TCTTTAAGTTCATTGGGTTCCACC 59.169 41.667 0.00 0.00 37.60 4.61
1836 1930 4.522789 GGGCCATTGAGTTGTTCTTCTTTA 59.477 41.667 4.39 0.00 0.00 1.85
1839 1934 2.108952 AGGGCCATTGAGTTGTTCTTCT 59.891 45.455 6.18 0.00 0.00 2.85
1840 1935 2.489722 GAGGGCCATTGAGTTGTTCTTC 59.510 50.000 6.18 0.00 0.00 2.87
1843 1938 1.909700 TGAGGGCCATTGAGTTGTTC 58.090 50.000 6.18 0.00 0.00 3.18
1893 1988 1.089920 CACACTACAGGCTCAATGGC 58.910 55.000 0.00 0.00 42.15 4.40
1894 1989 2.479566 ACACACTACAGGCTCAATGG 57.520 50.000 0.00 0.00 0.00 3.16
1895 1990 3.928992 CACTACACACTACAGGCTCAATG 59.071 47.826 0.00 0.00 0.00 2.82
1896 1991 3.055819 CCACTACACACTACAGGCTCAAT 60.056 47.826 0.00 0.00 0.00 2.57
1897 1992 2.299013 CCACTACACACTACAGGCTCAA 59.701 50.000 0.00 0.00 0.00 3.02
1898 1993 1.893137 CCACTACACACTACAGGCTCA 59.107 52.381 0.00 0.00 0.00 4.26
1899 1994 2.094649 GTCCACTACACACTACAGGCTC 60.095 54.545 0.00 0.00 0.00 4.70
1900 1995 1.893801 GTCCACTACACACTACAGGCT 59.106 52.381 0.00 0.00 0.00 4.58
1901 1996 1.616865 TGTCCACTACACACTACAGGC 59.383 52.381 0.00 0.00 31.43 4.85
1912 2007 2.267961 CCCGGGCTTGTCCACTAC 59.732 66.667 8.08 0.00 36.21 2.73
1924 2019 3.234630 TTCAACGAGCAGTCCCGGG 62.235 63.158 16.85 16.85 0.00 5.73
2063 2158 8.239038 TGGTGTTACTAAAATGTTCCATCAAA 57.761 30.769 0.00 0.00 0.00 2.69
2064 2159 7.825331 TGGTGTTACTAAAATGTTCCATCAA 57.175 32.000 0.00 0.00 0.00 2.57
2069 2164 7.039993 AGTCCATTGGTGTTACTAAAATGTTCC 60.040 37.037 1.86 0.00 0.00 3.62
2111 2206 2.519302 CACCCAATCCATCCGGCC 60.519 66.667 0.00 0.00 0.00 6.13
2116 2211 2.094675 CACAGAACCACCCAATCCATC 58.905 52.381 0.00 0.00 0.00 3.51
2174 2269 2.872245 CCGGTGCACTTACATTATCCAG 59.128 50.000 17.98 0.00 0.00 3.86
2295 3155 2.424956 GGGCTCTCTTTGGCACTAAATG 59.575 50.000 0.00 0.00 0.00 2.32


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.